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E3MFGYR02_alt_index_at_end.sff
E3MFGYR02_alt_index_at_start.sff
E3MFGYR02_alt_index_in_middle.sff
E3MFGYR02_index_at_start.sff
E3MFGYR02_index_in_middle.sff
E3MFGYR02_no_manifest.sff
E3MFGYR02_random_10_reads.fasta
E3MFGYR02_random_10_reads.qual
E3MFGYR02_random_10_reads.sff
E3MFGYR02_random_10_reads.sff.gz
E3MFGYR02_random_10_reads_no_trim.fasta
E3MFGYR02_random_10_reads_no_trim.qual
README.txt
greek.sff
invalid_greek_E3MFGYR02.sff
invalid_paired_E3MFGYR02.sff
paired.sff
triple_sff.idx
triple_sff_rel_paths.idx

README.txt

Created with Roche tools from E3MFGYR02.sff, extracting 10 random reads:

* E3MFGYR02_random_10_reads.sff - has an .mft1.00 style index and manifest
* E3MFGYR02_random_10_reads.fasta
* E3MFGYR02_random_10_reads.qual
* E3MFGYR02_random_10_reads_no_trim.fasta
* E3MFGYR02_random_10_reads_no_trim.qual
* E3MFGYR02_no_manifest.sff - has an .srt1.00 style index and no manifest

Modified with a dummy index block in various positions, SFF software
should ignore an unknown index block gracefully. The Roche tools are
happy to read these files:

* E3MFGYR02_alt_index_at_start.sff
* E3MFGYR02_alt_index_in_middle.sff
* E3MFGYR02_alt_index_at_end.sff

Modified to move the ".mft1.00" index block. The Roche tools do not
like these files, and Roche told me in an email exchange that their
(undocumented) index blocks should only be at the end of the file.
However, I still found these useful for testing:

* E3MFGYR02_index_at_start.sff
* E3MFGYR02_index_in_middle.sff

Additional SFF files modified from real data to rename the reads. The
Roche tools are happy to read these files. They make excellent tests
for parsing the index block since the read names are different lengths:

* greek.sff  - has an .srt1.00 style index
* paired.sff - has an .mft1.00 style index and manifest

Finally these file are concatenations of the greek.sff and paired.sff
files with E3MFGYR02_no_manifest.sff (for testing this as a special
error condition):

* invalid_greek_E3MFGYR02.sff - Concatenating SFF files together
* invalid_paired_E3MFGYR02.sff - Concatenating without 8 byte alignment